Working Results2
Kaushik Narasimhan
Sys.Date()
Summary Statistics
Species Information
## Species Mammal.Bird
## 1 agouti Mammal
## 2 brown four-eyed oppossum Mammal
## 3 crab eating racoon Mammal
## 4 coati Mammal
## 5 collared peccary Mammal
## 6 Greater Tinamou Bird
## 7 kinkajou Mammal
## 8 opossum Mammal
## 9 paca Mammal
## 10 red brocket deer Mammal
## 11 rufous fronted wood-quail (Odontophorus erythrops) Bird
## 12 rodent spp. Mammal
## 13 rufous tree rat Mammal
## 14 squirrel spp. Mammal
## 15 Tomes spiny rat Mammal
## 16 Wood-rail Bird
## Disperser. Func.group Animals. sightings ingestions removals nibbles
## 1 y TD ago 260 0 44 70
## 2 y TD bfo 82 2 2 4
## 3 y TD cer 1 0 0 0
## 4 y TD coa 458 2 0 175
## 5 y TD cpec 136 4 0 0
## 6 y TD gtin 8 0 0 0
## 7 y TD kink 84 0 3 14
## 8 y TD opos 100 1 0 27
## 9 y TD paca 416 0 31 73
## 10 y TD rbd 5 0 0 0
## 11 y TD rfw 434 0 0 4
## 12 y TD rod 1380 0 197 45
## 13 y TD rtr 5 0 0 1
## 14 y TD squ 675 0 249 109
## 15 y TD tsr 136 0 24 1
## 16 y TD wood-rail 127 0 0 7
## detections
## 1 15
## 2 12
## 3 1
## 4 11
## 5 7
## 6 2
## 7 9
## 8 8
## 9 10
## 10 1
## 11 15
## 12 21
## 13 1
## 14 20
## 15 6
## 16 10Visualization of visitation and dispersal trends against phenology
NFM is the number of mature fruits on a tree. The levels are as follows:
- a: 1- 50
- b: 51 - 200
- c: 201 - 500
- d: 501 - 1000
- e: 1001 - 5000
- f: 5000+
The below charts are the NFM compared with real visitation. The X axis is each “tree month” that had a camera in it. The X axis is in sequential order from earliest to latest. It has both high and low cameras.
This doesnt reveal too much in the way of relationships. Lets extract trees that occur across consecutive months.
Visualization of ht vs focal 50
Histograms of 50m bands
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.00 4.00 19.50 34.28 41.00 237.00## [1] 1962.388## Best Normalizing transformation with 162 Observations
## Estimated Normality Statistics (Pearson P / df, lower => more normal):
## - No transform: 3.4629
## - Log_b(x+a): 3.6176
## - sqrt(x+a): 1.2309
## - exp(x): 5.7714
## - arcsinh(x): 1.4514
## - Yeo-Johnson: 1.0713
## - orderNorm: 1.208
## Estimation method: Out-of-sample via CV with 10 folds and 5 repeats
##
## Based off these, bestNormalize chose:
## Standardized Yeo-Johnson Transformation with 162 nonmissing obs.:
## Estimated statistics:
## - lambda = 0.1337981
## - mean (before standardization) = 3.458438
## - sd (before standardization) = 2.135431Scatter plots using 50m
Scatter of Disperser visitation at 50m fruiting neighborhood
Scatter of Disperser visitation at 50m fruiting neighborhood at high cameras
Scatter of Dispersal at low cameras
Correlation at each band
effect of height focal against visitation
## $vis.rate
##
## $FD.rate
##
## $TD.rate
PCA of all environmental variables
PCA of selected environmental variables
Models 50 m band
## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula:
## real.visitation ~ focalmonth..50 * Height + (1 + focalmonth..50 |
## Tree)
## Data: cam_data_NFM1tree
##
## AIC BIC logLik deviance df.resid
## 3854.7 3876.3 -1920.4 3840.7 154
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -9.4056 -2.5120 -0.4039 1.4000 25.8977
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## Tree (Intercept) 2.047 1.431
## focalmonth..50 1.466 1.211 -0.57
## Number of obs: 161, groups: Tree, 49
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 2.10935 0.22237 9.486 < 2e-16 ***
## focalmonth..50 0.49940 0.30408 1.642 0.101
## Heightlow 0.93455 0.04358 21.445 < 2e-16 ***
## focalmonth..50:Heightlow -0.31323 0.03818 -8.204 2.32e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) fc..50 Hghtlw
## fclmnth..50 -0.424
## Heightlow -0.155 0.068
## fclmn..50:H 0.096 -0.098 -0.633## chisq ratio rdf p
## 2959.73756 19.21908 154.00000 0.00000## df.resid
## 19.21908##
## PARAMETRIC BOOTSTRAP
##
##
## Call:
## bootMer(x = model.9, FUN = FUN, nsim = 100)
##
##
## Bootstrap Statistics :
## original bias std. error
## t1* 2959.738 -2858.498 14.45909## 2.5% 97.5%
## 29.83737 22.53453 39.87581## df.resid
## 19.21908## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: real.visitation ~ focalmonth..50 * Height + (1 | obs_effect) +
## (1 + focalmonth..50 | Tree)
## Data: cam_data_NFM1tree
##
## AIC BIC logLik deviance df.resid
## 1454.4 1479.1 -719.2 1438.4 153
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.17365 -0.18972 0.02925 0.07302 0.26186
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## obs_effect (Intercept) 1.97138 1.4041
## Tree (Intercept) 0.60808 0.7798
## focalmonth..50 0.03535 0.1880 -1.00
## Number of obs: 161, groups: obs_effect, 161; Tree, 49
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.7366 0.2751 6.313 2.74e-10 ***
## focalmonth..50 0.1999 0.2001 0.999 0.318
## Heightlow 1.3203 0.2942 4.488 7.20e-06 ***
## focalmonth..50:Heightlow -0.2569 0.2435 -1.055 0.291
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) fc..50 Hghtlw
## fclmnth..50 -0.537
## Heightlow -0.715 0.423
## fclmn..50:H 0.361 -0.767 -0.531
## convergence code: 0
## boundary (singular) fit: see ?isSingular## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: real.visitation ~ focalmonth..50 * Height + offset(lograte) +
## (1 + focalmonth..50 | Tree)
## Data: cam_data_NFM1tree
##
## AIC BIC logLik deviance df.resid
## 3794.0 3815.6 -1890.0 3780.0 154
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -8.5540 -2.5265 -0.5044 1.5826 30.3127
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## Tree (Intercept) 2.055 1.433
## focalmonth..50 1.286 1.134 -0.59
## Number of obs: 161, groups: Tree, 49
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -0.33897 0.22232 -1.525 0.1273
## focalmonth..50 0.51673 0.28594 1.807 0.0707 .
## Heightlow 0.85862 0.04317 19.889 < 2e-16 ***
## focalmonth..50:Heightlow -0.27907 0.03740 -7.462 8.5e-14 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) fc..50 Hghtlw
## fclmnth..50 -0.435
## Heightlow -0.154 0.070
## fclmn..50:H 0.094 -0.101 -0.625## chisq ratio rdf p
## 3111.07009 20.20175 154.00000 0.00000## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula:
## real.visitation ~ focalmonth..50 + offset(lograte) + (1 | obs_effect) +
## (1 + focalmonth..50 | Tree)
## Data: cam_data_NFM1tree
##
## AIC BIC logLik deviance df.resid
## 1469.5 1488.0 -728.8 1457.5 155
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.18093 -0.18346 0.01850 0.06333 0.17155
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## obs_effect (Intercept) 2.27529 1.5084
## Tree (Intercept) 0.59520 0.7715
## focalmonth..50 0.05837 0.2416 -1.00
## Number of obs: 161, groups: obs_effect, 161; Tree, 49
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.128395 0.198866 0.646 0.519
## focalmonth..50 0.004476 0.135904 0.033 0.974
##
## Correlation of Fixed Effects:
## (Intr)
## fclmnth..50 -0.587
## convergence code: 0
## boundary (singular) fit: see ?isSingular## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -0.339 0.999 -0.34 0.734
## focalmonth..50 0.517 1.285 0.40 0.688
## Heightlow 0.859 0.194 4.43 9.6e-06 ***
## focalmonth..50:Heightlow -0.279 0.168 -1.66 0.097 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: real.visitation ~ focalmonth..50 * Height + offset(lograte) +
## (1 + focalmonth..50 | Tree)
## Data: cam_data_NFM1tree
##
## AIC BIC logLik deviance df.resid
## 3794.0 3815.6 -1890.0 3780.0 154
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -8.5540 -2.5265 -0.5044 1.5826 30.3127
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## Tree (Intercept) 2.055 1.433
## focalmonth..50 1.286 1.134 -0.59
## Number of obs: 161, groups: Tree, 49
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -0.33897 0.22232 -1.525 0.1273
## focalmonth..50 0.51673 0.28594 1.807 0.0707 .
## Heightlow 0.85862 0.04317 19.889 < 2e-16 ***
## focalmonth..50:Heightlow -0.27907 0.03740 -7.462 8.5e-14 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) fc..50 Hghtlw
## fclmnth..50 -0.435
## Heightlow -0.154 0.070
## fclmn..50:H 0.094 -0.101 -0.625## chisq ratio rdf p
## 3111.07009 20.20175 154.00000 0.00000## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: real.visitation ~ focalmonth..50 * Height + offset(lograte) +
## (1 | obs_effect) + (1 + focalmonth..50 | Tree)
## Data: cam_data_NFM1tree
##
## AIC BIC logLik deviance df.resid
## 1454.6 1479.2 -719.3 1438.6 153
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.16823 -0.19820 0.02129 0.07651 0.31996
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## obs_effect (Intercept) 1.93269 1.3902
## Tree (Intercept) 0.71153 0.8435
## focalmonth..50 0.05528 0.2351 -1.00
## Number of obs: 161, groups: obs_effect, 161; Tree, 49
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -0.6735 0.2793 -2.411 0.0159 *
## focalmonth..50 0.1535 0.2008 0.765 0.4445
## Heightlow 1.2254 0.2929 4.183 2.87e-05 ***
## focalmonth..50:Heightlow -0.2117 0.2415 -0.876 0.3808
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) fc..50 Hghtlw
## fclmnth..50 -0.549
## Heightlow -0.705 0.422
## fclmn..50:H 0.360 -0.768 -0.533
## convergence code: 0
## boundary (singular) fit: see ?isSingular## [1] FALSE## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -0.339 0.999 -0.34 0.734
## focalmonth..50 0.517 1.285 0.40 0.688
## Heightlow 0.859 0.194 4.43 9.6e-06 ***
## focalmonth..50:Heightlow -0.279 0.168 -1.66 0.097 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula:
## real.visitation ~ focalmonth..50 * Height + PC1 + PC2 + offset(lograte) +
## (1 + focalmonth..50 | Tree)
## Data: cam_data_NFM1tree
##
## AIC BIC logLik deviance df.resid
## 3796.5 3824.2 -1889.2 3778.5 152
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -8.5525 -2.5302 -0.4724 1.5840 30.3134
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## Tree (Intercept) 1.994 1.412
## focalmonth..50 1.274 1.129 -0.59
## Number of obs: 161, groups: Tree, 49
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -0.29970 0.22185 -1.351 0.1767
## focalmonth..50 0.54920 0.28470 1.929 0.0537 .
## Heightlow 0.85941 0.04317 19.906 < 2e-16 ***
## PC1 -0.60178 0.52215 -1.153 0.2491
## PC2 0.17118 0.55214 0.310 0.7565
## focalmonth..50:Heightlow -0.27945 0.03740 -7.472 7.87e-14 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) fc..50 Hghtlw PC1 PC2
## fclmnth..50 -0.420
## Heightlow -0.152 0.071
## PC1 -0.085 -0.087 -0.011
## PC2 0.111 0.006 0.005 0.149
## fclmn..50:H 0.093 -0.102 -0.625 0.005 -0.004## chisq ratio rdf p
## 3110.79632 20.46577 152.00000 0.00000## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula:
## real.visitation ~ focalmonth..50 * Height + PC1 + PC2 + offset(lograte) +
## (1 | obs_effect) + (1 + focalmonth..50 | Tree)
## Data: cam_data_NFM1tree
##
## AIC BIC logLik deviance df.resid
## 1454.8 1485.7 -717.4 1434.8 151
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.14622 -0.17623 0.01037 0.07654 0.30887
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## obs_effect (Intercept) 1.96058 1.4002
## Tree (Intercept) 0.51627 0.7185
## focalmonth..50 0.05093 0.2257 -1.00
## Number of obs: 161, groups: obs_effect, 161; Tree, 49
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -0.70493 0.27021 -2.609 0.00909 **
## focalmonth..50 0.19819 0.21010 0.943 0.34551
## Heightlow 1.26906 0.29437 4.311 1.62e-05 ***
## PC1 -0.81832 0.40337 -2.029 0.04249 *
## PC2 -0.05268 0.41998 -0.125 0.90019
## focalmonth..50:Heightlow -0.21157 0.24402 -0.867 0.38593
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) fc..50 Hghtlw PC1 PC2
## fclmnth..50 -0.552
## Heightlow -0.727 0.429
## PC1 0.097 -0.127 -0.096
## PC2 -0.069 0.199 0.078 0.060
## fclmn..50:H 0.380 -0.767 -0.535 0.009 -0.102
## convergence code: 0
## Model failed to converge with max|grad| = 0.00378545 (tol = 0.001, component 1)Models using functional groups
## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula:
## TD ~ focalmonth..50 * Height + offset(lograte) + (1 + focalmonth..50 |
## Tree)
## Data: cam_data_NFM1tree
##
## AIC BIC logLik deviance df.resid
## 2472.5 2494.0 -1229.2 2458.5 154
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -6.9756 -1.9011 -0.5447 0.9866 15.3002
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## Tree (Intercept) 2.188 1.479
## focalmonth..50 1.378 1.174 -0.58
## Number of obs: 161, groups: Tree, 49
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -2.22943 0.24407 -9.134 <2e-16 ***
## focalmonth..50 0.51793 0.30635 1.691 0.0909 .
## Heightlow 2.78539 0.09157 30.417 <2e-16 ***
## focalmonth..50:Heightlow -0.55727 0.05722 -9.739 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) fc..50 Hghtlw
## fclmnth..50 -0.430
## Heightlow -0.335 0.118
## fclmn..50:H 0.225 -0.170 -0.674## chisq ratio rdf p
## 1.875957e+03 1.218154e+01 1.540000e+02 1.945129e-293## boundary (singular) fit: see ?isSingular## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula:
## TD ~ focalmonth..50 * Height + offset(lograte) + (1 | obs_effect) +
## (1 + focalmonth..50 | Tree)
## Data: cam_data_NFM1tree
##
## AIC BIC logLik deviance df.resid
## 1212.7 1237.3 -598.3 1196.7 153
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.13110 -0.48719 -0.01168 0.05818 0.50225
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## obs_effect (Intercept) 2.2421084 1.49737
## Tree (Intercept) 0.2955314 0.54363
## focalmonth..50 0.0002012 0.01418 -1.00
## Number of obs: 161, groups: obs_effect, 161; Tree, 49
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -3.0786 0.3369 -9.139 <2e-16 ***
## focalmonth..50 0.4197 0.2493 1.684 0.0922 .
## Heightlow 3.5915 0.3652 9.834 <2e-16 ***
## focalmonth..50:Heightlow -0.4993 0.2814 -1.774 0.0760 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) fc..50 Hghtlw
## fclmnth..50 -0.490
## Heightlow -0.829 0.431
## fclmn..50:H 0.415 -0.787 -0.533
## convergence code: 0
## boundary (singular) fit: see ?isSingular## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: TD ~ focalmonth..50 * Height + PC1 + PC2 + offset(lograte) +
## (1 + focalmonth..50 | Tree)
## Data: cam_data_NFM1tree
##
## AIC BIC logLik deviance df.resid
## 2475.6 2503.4 -1228.8 2457.6 152
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -6.9740 -1.9018 -0.5431 0.9820 15.3044
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## Tree (Intercept) 2.128 1.459
## focalmonth..50 1.387 1.178 -0.58
## Number of obs: 161, groups: Tree, 49
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -2.21188 0.24443 -9.049 <2e-16 ***
## focalmonth..50 0.54814 0.31057 1.765 0.0776 .
## Heightlow 2.78624 0.09158 30.423 <2e-16 ***
## PC1 -0.50126 0.54527 -0.919 0.3580
## PC2 -0.07591 0.58422 -0.130 0.8966
## focalmonth..50:Heightlow -0.55755 0.05722 -9.744 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) fc..50 Hghtlw PC1 PC2
## fclmnth..50 -0.410
## Heightlow -0.334 0.117
## PC1 -0.063 -0.099 -0.008
## PC2 0.130 -0.007 0.002 0.166
## fclmn..50:H 0.224 -0.168 -0.674 0.004 -0.002## chisq ratio rdf p
## 1.876307e+03 1.234413e+01 1.520000e+02 1.339943e-294## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: TD ~ focalmonth..50 * Height + PC1 + PC2 + offset(lograte) +
## (1 | obs_effect) + (1 + focalmonth..50 | Tree)
## Data: cam_data_NFM1tree
##
## AIC BIC logLik deviance df.resid
## 1215.8 1246.6 -597.9 1195.8 151
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.13460 -0.47661 -0.01578 0.05759 0.54638
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## obs_effect (Intercept) 2.244951 1.49832
## Tree (Intercept) 0.295418 0.54352
## focalmonth..50 0.004569 0.06759 -1.00
## Number of obs: 161, groups: obs_effect, 161; Tree, 49
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -3.0918 0.3389 -9.123 <2e-16 ***
## focalmonth..50 0.4388 0.2457 1.786 0.0741 .
## Heightlow 3.6066 0.3672 9.821 <2e-16 ***
## PC1 -0.3621 0.4243 -0.853 0.3935
## PC2 -0.1752 0.4226 -0.415 0.6784
## focalmonth..50:Heightlow -0.4951 0.2792 -1.773 0.0762 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) fc..50 Hghtlw PC1 PC2
## fclmnth..50 -0.517
## Heightlow -0.831 0.455
## PC1 0.105 -0.147 -0.099
## PC2 -0.052 0.148 0.055 0.040
## fclmn..50:H 0.419 -0.790 -0.536 0.015 -0.074
## convergence code: 0
## Model failed to converge with max|grad| = 0.0201813 (tol = 0.001, component 1)## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula:
## FD ~ focalmonth..50 * Height + offset(lograte) + (1 + focalmonth..50 |
## Tree)
## Data: cam_data_NFM1tree
##
## AIC BIC logLik deviance df.resid
## 1418.5 1440.0 -702.2 1404.5 154
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -7.7849 -0.9043 -0.3278 -0.0660 17.7018
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## Tree (Intercept) 4.116 2.029
## focalmonth..50 3.261 1.806 -0.57
## Number of obs: 161, groups: Tree, 49
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.4797 0.4284 -3.454 0.000552 ***
## focalmonth..50 0.9519 0.5925 1.607 0.108160
## Heightlow -2.4997 0.1449 -17.253 < 2e-16 ***
## focalmonth..50:Heightlow -1.4009 0.3249 -4.311 1.62e-05 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) fc..50 Hghtlw
## fclmnth..50 -0.457
## Heightlow -0.152 0.091
## fclmn..50:H 0.057 -0.216 -0.356## chisq ratio rdf p
## 1.221939e+03 7.934669e+00 1.540000e+02 1.509856e-165## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula:
## FD ~ focalmonth..50 * Height + offset(lograte) + (1 | obs_effect) +
## (1 + focalmonth..50 | Tree)
## Data: cam_data_NFM1tree
##
## AIC BIC logLik deviance df.resid
## 616.3 640.9 -300.1 600.3 153
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -0.74665 -0.24478 -0.13522 0.03046 1.25134
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## obs_effect (Intercept) 4.224 2.055
## Tree (Intercept) 2.543 1.595
## focalmonth..50 2.750 1.658 -0.62
## Number of obs: 161, groups: obs_effect, 161; Tree, 49
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.6706 0.5090 -3.282 0.00103 **
## focalmonth..50 0.9038 0.7170 1.260 0.20751
## Heightlow -3.5565 0.6225 -5.714 1.11e-08 ***
## focalmonth..50:Heightlow -1.7915 0.9480 -1.890 0.05880 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) fc..50 Hghtlw
## fclmnth..50 -0.490
## Heightlow -0.445 0.309
## fclmn..50:H 0.286 -0.624 -0.472## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: FD ~ focalmonth..50 * Height + PC1 + PC2 + offset(lograte) +
## (1 + focalmonth..50 | Tree)
## Data: cam_data_NFM1tree
##
## AIC BIC logLik deviance df.resid
## 1416.4 1444.1 -699.2 1398.4 152
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -7.7897 -0.9224 -0.3045 -0.0663 17.6837
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## Tree (Intercept) 3.741 1.934
## focalmonth..50 2.633 1.623 -0.49
## Number of obs: 161, groups: Tree, 49
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.4788 0.4146 -3.567 0.000361 ***
## focalmonth..50 1.1028 0.5845 1.887 0.059190 .
## Heightlow -2.4796 0.1437 -17.260 < 2e-16 ***
## PC1 -1.8091 0.8246 -2.194 0.028250 *
## PC2 0.7492 0.9920 0.755 0.450096
## focalmonth..50:Heightlow -1.3933 0.3195 -4.361 1.29e-05 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) fc..50 Hghtlw PC1 PC2
## fclmnth..50 -0.449
## Heightlow -0.137 0.083
## PC1 0.199 -0.210 -0.043
## PC2 -0.014 -0.069 0.028 0.069
## fclmn..50:H 0.051 -0.208 -0.354 0.008 0.044
## convergence code: 0
## Model failed to converge with max|grad| = 0.116505 (tol = 0.001, component 1)## chisq ratio rdf p
## 1.207626e+03 7.944906e+00 1.520000e+02 9.953175e-164## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: FD ~ focalmonth..50 * Height + PC1 + PC2 + offset(lograte) +
## (1 | obs_effect) + (1 + focalmonth..50 | Tree)
## Data: cam_data_NFM1tree
##
## AIC BIC logLik deviance df.resid
## 617.8 648.6 -298.9 597.8 151
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -0.75059 -0.24345 -0.13438 0.02927 1.12468
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## obs_effect (Intercept) 4.036 2.009
## Tree (Intercept) 2.481 1.575
## focalmonth..50 2.641 1.625 -0.55
## Number of obs: 161, groups: obs_effect, 161; Tree, 49
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.7796 0.5074 -3.507 0.000453 ***
## focalmonth..50 1.0650 0.7256 1.468 0.142195
## Heightlow -3.4061 0.6159 -5.530 3.19e-08 ***
## PC1 -1.1574 0.8326 -1.390 0.164501
## PC2 0.6826 0.9919 0.688 0.491383
## focalmonth..50:Heightlow -1.8434 0.9596 -1.921 0.054728 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) fc..50 Hghtlw PC1 PC2
## fclmnth..50 -0.482
## Heightlow -0.448 0.308
## PC1 0.152 -0.097 -0.044
## PC2 -0.106 0.121 0.073 0.011
## fclmn..50:H 0.275 -0.614 -0.475 -0.043 -0.100
## convergence code: 0
## Model failed to converge with max|grad| = 0.180158 (tol = 0.001, component 1)## bobyqa : [OK]
## Nelder_Mead : [OK]
## nlminbwrap : [OK]
## nmkbw : [OK]
## optimx.L-BFGS-B : [OK]
## nloptwrap.NLOPT_LN_NELDERMEAD : [OK]
## nloptwrap.NLOPT_LN_BOBYQA : [OK]## bobyqa Nelder_Mead
## TRUE TRUE
## nlminbwrap nmkbw
## TRUE TRUE
## optimx.L-BFGS-B nloptwrap.NLOPT_LN_NELDERMEAD
## FALSE TRUE
## nloptwrap.NLOPT_LN_BOBYQA
## TRUE## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: poisson ( log )
## Formula: FD ~ focalmonth..50 * Height + PC1 + PC2 + offset(lograte) +
## (1 | obs_effect) + (1 + focalmonth..50 | Tree)
## Data: cam_data_NFM1tree
##
## AIC BIC logLik deviance df.resid
## 617.7 648.5 -298.9 597.7 151
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -0.7394 -0.2434 -0.1376 0.0277 1.0980
##
## Random effects:
## Groups Name Variance Std.Dev. Corr
## obs_effect (Intercept) 4.113 2.028
## Tree (Intercept) 2.224 1.491
## focalmonth..50 2.343 1.531 -0.50
## Number of obs: 161, groups: obs_effect, 161; Tree, 49
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -1.7793 0.4997 -3.561 0.00037 ***
## focalmonth..50 1.0424 0.7219 1.444 0.14873
## Heightlow -3.3946 0.6151 -5.519 3.42e-08 ***
## PC1 -1.1523 0.8079 -1.426 0.15379
## PC2 0.6750 0.9730 0.694 0.48786
## focalmonth..50:Heightlow -1.8380 0.9594 -1.916 0.05539 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) fc..50 Hghtlw PC1 PC2
## fclmnth..50 -0.468
## Heightlow -0.455 0.314
## PC1 0.154 -0.097 -0.050
## PC2 -0.112 0.125 0.077 0.008
## fclmn..50:H 0.276 -0.623 -0.475 -0.033 -0.104
## convergence code: 0
## Model failed to converge with max|grad| = 0.0180262 (tol = 0.001, component 1)